BBMRI

Feedback group:

• BBMRI steering committee
• Collaboration with Marco Roos (semweb interface + data on biobankers)

Tasks 1: Add LifeLines metadata (features/protocols)

Primary goal: get LifeLines features included in BBMRI biobank as example for other biobanks.

• get BBMRI catalog running - despoina (done)
• import the Excel - despoina (done)
• biobank is a kind of panel - despoina (done)
• Get from Joris is a Excel export of LifeLines biobank metadata - joris (features, protocols)
• update online version, and send email around to steering committe - morris

Task 2: Add biobank information from BBMR-EU

Primary goal: get european data into the catalog and expand model when needed

• contact the BBMRI-EU catalog (​http://gbic.target.rug.nl/trac/molgenis/wiki/BBMRI) - morris
• get data as csv or something similar - morris
• reformat csv to match features, protocols, biobanks, contacts, and update model if something is missing - despoina

Task 3: Add semantic search

Primary goal: to have the semantic search available for BBMRI catalog

Task 4: Add and improve sparql interface

Primary goal: make catalogue queriable by sparql

• Add and check the sparql interface - despoina
• Put it in the online version - despoina
• Ask Marco Roos to verify the endpoint and give feedback on it - marco
• Write short wiki page on how to use ​Pedro Lopes feedback - despoina

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Theme 2: start with 'semantic molgenis'

First goal: link MOLGENIS to external ontology

• first enhance N3 file with external mapping:

• then test if we use that ontology in SPARQL query

• if works: then update the MOLGENIS model + generator

Next step: investigate ontologies that should be linked

• how about biobankers list of Marco Roos?

• disease ontology?

• material ontology?

Actions

• Connect to Pedro to investigate his 'semantic molgenis' work?

• Connect to BBMRI-EU to request more data?

(Notes)

• look into data
• cross links —> protein underlying peaks ?
• biobanks : phenotypic information e.g lifelines project data : annotate question : ARE there other data set in the world? —> merge into lifelines data …
• next step : come up with an "algorithm" that does the mapping . Let's assume we have 2 studies , we would like to merge and export the results .
• it's not really an algorithm , but more of a "correspondence " rule …If we have 2 questions - "Are they compatible "? or if not what kind of conversion should be done in order to match each other? So then we'll have a meta study ..for each biobank —> mapping
• So we have available 5 biobanks —> project on a single parameter —> bigger statistical analysis .
• How to model it ?
• RDF rules?
• parameter in one biobank / corresponding parameter in the other biobank ?
• a potential pilot would be like to

1. take 2 pheno DBs ,
2. fill with lifelines data ,
3. query that merges the set —> maybe a sparql query ?
4. different question